Supplementary Report S2. Report with ASV without OTU post-clustering. Terroir and farming practices drive arbuscular mycorrhizal fungal communities in French vineyard.
Min. 1st Qu. Median Mean 3rd Qu. Max.
2856 26872 36324 40116 48250 112831
Code
sd(sample_sums(d_asv))
[1] 19487.06
The samples with the lower nb of total sequences is 21MET828 (2856 seq.) but it contains only AMF sequences. So we keep all samples.
Code
hist(log10(sample_sums(d)), breaks =40)
Number of sequences per samples (AMF only)
Code
summary(sample_sums(d))
Min. 1st Qu. Median Mean 3rd Qu. Max.
837 12329 21866 25190 32704 91395
Code
sd(sample_sums(d))
[1] 17966.48
Summary of final dataset
Code
summary_plot_pq(d) +labs(title ="Summary of final dataset") +theme(plot.title =element_text(hjust =0.5, size =20, color ="#1e2b4c"))
Cleaning suppress 0 taxa and 0 samples.
Summary of bioinformatics pipeline
Global summary
Code
kable(tar_read(track_sequences_samples_clusters))
nb_sequences
nb_clusters
nb_samples
Paired sequences
8283717
28637
194
Paired sequences without chimera
7784063
10298
194
Paired sequences without chimera and longer than 200bp
7737954
7815
194
ASV denoising
7534699
7815
186
OTU after vsearch reclustering at 97%
7534699
1182
186
OTU after blast filter without reclustering
3821515
3916
182
OTU after blast filter with reclustering
3823905
239
182
# TAXONOMICAL ANALYSES
Code
# Fig S9multitax_bar_pq(d_asv, "Supergroup_PR2","Subdivision_PR2", "Class_PR2",nb_seq =TRUE) +ggtitle("Number of sequences (log10) including non-Mucoromycota")
Code
multitax_bar_pq(d_asv, "Supergroup_PR2","Subdivision_PR2", "Class_PR2",nb_seq =FALSE,log10trans =FALSE) +ggtitle("Number of OTUs including non-Mucoromycota")
df <-data.frame("Proportion of sequences"=c(round(sum(d_asv_blast@otu_table) /sum(d_asv@otu_table), 3 ),round(sum(d_muco@otu_table) /sum(d_asv@otu_table), 3 ) ),"Proportion of OTU"=c(round(ntaxa(d_asv_blast) /ntaxa(d_asv), 3 ),round(ntaxa(d_muco) /ntaxa(d_asv), 3 ) ))rownames(df) <-c("Blast filter on Maarjam","Add a filter on Mucoromycota family in PR2")kable(df)
After merging soil and root tips paired samples, the minimum nb of sequences per samples is 6768
Code
spores_roots_samples <-sample_names(d_asv_blast)[d_asv_blast@sam_data$compartment!="Mycelium"]tar_load(derep_fs)tar_load(seq_tab_Pairs)tar_load(seqtab_wo_chimera)tar_load(seqtab)tar_load(data_phyloseq_PR2)# TABLE XXX_pipelinetw <-track_wkflow(list("Raw data"=tar_read(data_raw)$fnfs[grepl(paste(spores_roots_samples, collapse='|'), tar_read(data_raw)$fnfs)],"Quality-filtered data"= derep_fs[grepl(paste(spores_roots_samples, collapse='|'),names(derep_fs))],"Paired denoised sequences (ASV)"= seq_tab_Pairs[grepl(paste(spores_roots_samples, collapse='|'),rownames(seq_tab_Pairs)),colSums(seq_tab_Pairs[grepl(paste(spores_roots_samples, collapse='|'),rownames(seq_tab_Pairs)),])>0],# "ASV without chimera" = seqtab_wo_chimera[grepl(paste(spores_roots_samples, collapse='|'),rownames(seqtab_wo_chimera)),],"ASV without chimera and longer than 200bp"= seqtab[grepl(paste(spores_roots_samples, collapse='|'),rownames(seqtab)),colSums(seqtab[grepl(paste(spores_roots_samples, collapse='|'),rownames(seqtab)),])>0],"OTU after vsearch reclustering at 97%"=clean_pq(subset_samples(tar_read(data_phyloseq_PR2), compartment !="Mycelium")),"Maarjam Filtered"=clean_pq(subset_samples(tar_read(d_blast), compartment !="Mycelium")),"PR2 Filtered"= d_muco,"Roots only"= d_roots,"Spores only"= d_spores,"Roots + spores merged"= d_rs_merged_samples ))
Compute the number of sequences
Cleaning suppress 1836 taxa and 0 samples.
Cleaning suppress 117 taxa and 0 samples.
Start object of class: character
Start object of class: list
Start object of class: matrixStart object of class: array
Start object of class: matrixStart object of class: array
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Compute the number of clusters
Start object of class: character
Start object of class: list
Start object of class: matrixStart object of class: array
Start object of class: matrixStart object of class: array
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Compute the number of samples
Start object of class: character
Start object of class: list
Start object of class: matrixStart object of class: array
Start object of class: matrixStart object of class: array
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
# Fig S2aggstatsplot::ggscatterstats(psm_res, nb_spores_log10, Abundance, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res, nb_spores_log10, Hill_0, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res, nb_spores_log10, Hill_1, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res, nb_spores_log10, Hill_2, type ="non-parametric")
Registered S3 method overwritten by 'ggside':
method from
+.gg ggplot2
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`set.seed(221013)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(221013); .Random.seed` for the full vector
...
490OTUs were removed because they are no longer
present in any sample after random subsampling
...
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Code
ggstatsplot::ggscatterstats(psm_res_rarefied, nb_spores_log10, Abundance, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res_rarefied, nb_spores_log10, Hill_0, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res_rarefied, nb_spores_log10, Hill_1, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res_rarefied, nb_spores_log10, Hill_2, type ="non-parametric")
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
ggstatsplot::ggscatterstats(psm_res_rarefied, nb_spores_log10, Myc_freq, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res_rarefied, nb_spores_log10, Myc_intensity_colonization, type ="non-parametric") + ggstatsplot::ggscatterstats(psm_res_rarefied, nb_spores_log10, Arbuscul_abundance, type ="non-parametric")
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`set.seed(221013)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(221013); .Random.seed` for the full vector
...
1269OTUs were removed because they are no longer
present in any sample after random subsampling
...
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Code
# Fig S3a(ggstatsplot::ggscatterstats(psm_res, Myc_freq, Hill_0, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res, Myc_freq, Hill_1, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res, Myc_freq, Hill_2, type ="non-parametrique")) / (ggstatsplot::ggscatterstats(psm_res_rarefied, Myc_freq, Hill_0, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res_rarefied, Myc_freq, Hill_1, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res_rarefied, Myc_freq, Hill_2, type ="non-parametrique"))
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
M = Myc_intensity_colonization
Code
# Fig S3b(ggstatsplot::ggscatterstats(psm_res, Myc_intensity_colonization, Hill_0, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res, Myc_intensity_colonization, Hill_1, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res, Myc_intensity_colonization, Hill_2, type ="non-parametrique")) / (ggstatsplot::ggscatterstats(psm_res_rarefied, Myc_intensity_colonization, Hill_0, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res_rarefied, Myc_intensity_colonization, Hill_1, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res_rarefied, Myc_intensity_colonization, Hill_2, type ="non-parametrique"))
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
A = Arbuscul_abundance
Code
# Fig S3c(ggstatsplot::ggscatterstats(psm_res, Arbuscul_abundance , Hill_0, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res, Arbuscul_abundance, Hill_1, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res, Arbuscul_abundance, Hill_2, type ="non-parametrique")) / (ggstatsplot::ggscatterstats(psm_res_rarefied, Arbuscul_abundance, Hill_0, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res_rarefied, Arbuscul_abundance, Hill_1, type ="non-parametrique") + ggstatsplot::ggscatterstats(psm_res_rarefied, Arbuscul_abundance, Hill_2, type ="non-parametrique"))
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
Mycorrhization rate <-> terroir
Code
ggstatsplot::ggbetweenstats(psm_res_rarefied, terroir, Myc_freq, type ="non-parametrique", centrality.plotting = F) + ggstatsplot::ggbetweenstats(psm_res_rarefied, terroir, Myc_intensity_colonization, type ="non-parametrique", centrality.plotting = F) + ggstatsplot::ggbetweenstats(psm_res_rarefied, terroir, Arbuscul_abundance, type ="non-parametrique", centrality.plotting = F)
Number of labels is greater than default palette color count.
• Select another color `palette` (and/or `package`).
Number of labels is greater than default palette color count.
• Select another color `palette` (and/or `package`).
Number of labels is greater than default palette color count.
• Select another color `palette` (and/or `package`).
`set.seed(221013)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(221013); .Random.seed` for the full vector
...
1969OTUs were removed because they are no longer
present in any sample after random subsampling
...
Taxa are now in rows.
Joining with `by = join_by(Sample)`
`set.seed(221013)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(221013); .Random.seed` for the full vector
...
1269OTUs were removed because they are no longer
present in any sample after random subsampling
...
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Warning in phyloseq::plot_ordination(d_muco,
vegan::decorana(vegdist(as(otu_table(d_muco), : `Ordination species/OTU/taxa
coordinate indices did not match `physeq` index names. Setting corresponding
coordinates to NULL.
Code
p +geom_line(data = p$data, aes(group = paired_name))
Square root transformation
Wisconsin double standardization
Run 0 stress 0.2199813
Run 1 stress 0.2448036
Run 2 stress 0.2180221
... New best solution
... Procrustes: rmse 0.06822839 max resid 0.5284097
Run 3 stress 0.216845
... New best solution
... Procrustes: rmse 0.02068218 max resid 0.116768
Run 4 stress 0.2168451
... Procrustes: rmse 0.0002339127 max resid 0.001590561
... Similar to previous best
Run 5 stress 0.2199347
Run 6 stress 0.2381263
Run 7 stress 0.2176648
Run 8 stress 0.2206405
Run 9 stress 0.2199851
Run 10 stress 0.2177386
Run 11 stress 0.2382035
Run 12 stress 0.2505707
Run 13 stress 0.2186254
Run 14 stress 0.2260154
Run 15 stress 0.2168451
... Procrustes: rmse 0.0001809623 max resid 0.001056322
... Similar to previous best
Run 16 stress 0.2200828
Run 17 stress 0.225982
Run 18 stress 0.2488814
Run 19 stress 0.2168449
... New best solution
... Procrustes: rmse 0.0002316716 max resid 0.001384702
... Similar to previous best
Run 20 stress 0.2168451
... Procrustes: rmse 0.0002848589 max resid 0.001564728
... Similar to previous best
*** Best solution repeated 2 times
Code
p_nmds <- p +geom_point(data =select(p$data, -c(region)),fill ="grey40",color ="grey20",size =1,alpha =0.5) +geom_point(size =3, aes(fill=terroir)) +ggtitle("NMDS on bray distance") +scale_fill_manual(values=c("#5660d0","#de8a00","#b59e00","#00773d","#fcb709","#e15968","#784b43","#c200ab","#00b3f0","#953726","#e09199","#379d30","#ed5019","#ff63b0")) +scale_color_manual(values=rep("grey20",14))# XXXX_nmds_region_practice_terroirp_nmds
Code
p <- phyloseq::plot_ordination(d_rs,ordinate(d_rs,method ="NMDS",distance ="bray" ),color ="practice") +geom_point(size =4) +facet_wrap("~terroir")
Square root transformation
Wisconsin double standardization
Run 0 stress 0.2199813
Run 1 stress 0.2218407
Run 2 stress 0.2257996
Run 3 stress 0.2168451
... New best solution
... Procrustes: rmse 0.06699764 max resid 0.5255248
Run 4 stress 0.2201833
Run 5 stress 0.2182975
Run 6 stress 0.2505065
Run 7 stress 0.2183028
Run 8 stress 0.2222091
Run 9 stress 0.2205322
Run 10 stress 0.2256243
Run 11 stress 0.2198921
Run 12 stress 0.220747
Run 13 stress 0.228605
Run 14 stress 0.2279042
Run 15 stress 0.2201713
Run 16 stress 0.2182979
Run 17 stress 0.227071
Run 18 stress 0.219269
Run 19 stress 0.2168449
... New best solution
... Procrustes: rmse 0.0002240927 max resid 0.001403987
... Similar to previous best
Run 20 stress 0.2350719
*** Best solution repeated 1 times
Code
p +geom_point(data =select(p$data, -c(terroir)),size =2,alpha =0.3) +geom_point(size =4) +ggtitle("NMDS on bray distance")
Two modalities differ greatly (more than x2) in their number of sequences (1865101 vs 838771). You may be interested by the parameter rarefy_after_merging
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).
Analysis of Variance Table
Response: Distances
Df Sum Sq Mean Sq F value Pr(>F)
Groups 2 0.01743 0.0087135 0.8894 0.4154
Residuals 72 0.70541 0.0097974
`set.seed(626)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(626); .Random.seed` for the full vector
...
1258OTUs were removed because they are no longer
present in any sample after random subsampling
...
Analysis of Variance Table
Response: Distances
Df Sum Sq Mean Sq F value Pr(>F)
Groups 2 0.01743 0.0087135 0.8894 0.4154
Residuals 72 0.70541 0.0097974
Sampling bootstrap replicates... Please wait
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Comparing empirical statistics with their null distributions... Please wait
========================================================
Test of PCA significance: 17 variables, 49 observations
1000 bootstrap replicates, 1000 random permutations
========================================================
Empirical Psi = 57.6945, Max null Psi = 7.9011, Min null Psi = 3.9156, p-value = 0
Empirical Phi = 0.4606, Max null Phi = 0.1704, Min null Phi = 0.1200, p-value = 0
Empirical eigenvalue #1 = 7.79931, Max null eigenvalue = 2.7847, p-value = 0
Empirical eigenvalue #2 = 2.64507, Max null eigenvalue = 2.30548, p-value = 0
Empirical eigenvalue #3 = 1.91872, Max null eigenvalue = 2.00799, p-value = 0.009
Empirical eigenvalue #4 = 1.04069, Max null eigenvalue = 1.75936, p-value = 1
Empirical eigenvalue #5 = 0.90745, Max null eigenvalue = 1.56975, p-value = 1
Empirical eigenvalue #6 = 0.76203, Max null eigenvalue = 1.43569, p-value = 1
Empirical eigenvalue #7 = 0.61678, Max null eigenvalue = 1.30771, p-value = 1
Empirical eigenvalue #8 = 0.37522, Max null eigenvalue = 1.1816, p-value = 1
Empirical eigenvalue #9 = 0.25142, Max null eigenvalue = 1.09965, p-value = 1
Empirical eigenvalue #10 = 0.23602, Max null eigenvalue = 0.96987, p-value = 1
Empirical eigenvalue #11 = 0.18674, Max null eigenvalue = 0.8615, p-value = 1
Empirical eigenvalue #12 = 0.12613, Max null eigenvalue = 0.75665, p-value = 1
Empirical eigenvalue #13 = 0.08683, Max null eigenvalue = 0.70178, p-value = 1
Empirical eigenvalue #14 = 0.04197, Max null eigenvalue = 0.6121, p-value = 1
Empirical eigenvalue #15 = 0.00562, Max null eigenvalue = 0.52401, p-value = 1
Empirical eigenvalue #16 = 0, Max null eigenvalue = 0.41784, p-value = 1
Empirical eigenvalue #17 = 0, Max null eigenvalue = 0.37203, p-value = 1
PC 1 is significant and accounts for 45.9% (95%-CI:41.4-51.4) of the total variation
PC 2 is significant and accounts for 15.6% (95%-CI:13.7-19) of the total variation
PC 3 is significant and accounts for 11.3% (95%-CI:9-13.3) of the total variation
The first 3 PC axes are significant and account for 72.7% of the total variation
Variables 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, and 17 have significant loadings on PC 1
Variables 1, 4, 12, 13, and 16 have significant loadings on PC 2
Variables 3, 6, and 7 have significant loadings on PC 3
Variables 1, and 2 have significant correlations with PC 1
Variables 12, and 13 have significant correlations with PC 2
Variables 6, and 7 have significant correlations with PC 3
Code
pval <-c()for (i inseq_len(length(pca_test_res$`Percentage of variation of empirical PC's`))) { obs <- pca_test_res$`Percentage of variation of empirical PC's`[i] null_model <- pca_test_res$`Percentage of variation of randomized data`[, i] pval[i] <- (sum(obs < null_model) +1) / (1+nrow(pca_test_res$`Percentage of variation of randomized data`))}pca_test_pval_adj <-p.adjust(pval, method ="BH")pca_test_pval_adj
Scale for shape is already present.
Adding another scale for shape, which will replace the existing scale.
Code
p_pca_ind_terroir$data$terroir <- terroirp_pca_ind_terroir$data$practice <- practicep_pca_ind_terroir_practice <- p_pca_ind_terroir +geom_point(aes(x = x, y = y),shape =case_when( practice =="Organic"~2, practice =="Conventional"~6, practice =="Conversion"~5 ), size =3.5,color =rgb(0, 0, 0, 0.7))fviz_pca_var(res_pca)
Code
# valuekw1_terroir <-kruskal.test(res_pca$tab[, 1], terroir)kw2_terroir <-kruskal.test(res_pca$tab[, 2], terroir)kw3_terroir <-kruskal.test(res_pca$tab[, 3], terroir)kw1_practice <-kruskal.test(res_pca$tab[, 1], practice)kw2_practice <-kruskal.test(res_pca$tab[, 2], practice)kw3_practice <-kruskal.test(res_pca$tab[, 3], practice)# Fig. 3 -> now figure Sp_pca_ind_terroir_practice +annotate("text", x =2, y =4.5, label =paste("Kruskal-Wallis (axe1 - terroir): pval=", round(as.numeric(kw1_terroir$p.value),4)), size =3) +annotate("text", x =2, y =4.25, label =paste("Kruskal-Wallis (axe2 - terroir): pval=", round(as.numeric(kw2_terroir$p.value),4)), size =3) +annotate("text", x =2, y =4, label =paste("Kruskal-Wallis (axe3 - terroir): pval=", round(as.numeric(kw3_terroir$p.value),4)), size =3) +annotate("text", x =-2, y =4.5, label =paste("Kruskal-Wallis (axe1 - practice): pval=", round(as.numeric(kw1_practice$p.value),4)), size =3) +annotate("text", x =-2, y =4.25, label =paste("Kruskal-Wallis (axe2 - practice): pval=", round(as.numeric(kw2_practice$p.value),4)), size =3) +annotate("text", x =-2, y =4, label =paste("Kruskal-Wallis (axe3 - practice): pval=", round(as.numeric(kw3_practice$p.value),4)), size =3)
Warning: Removed 5 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 5 rows containing missing values or values outside the scale range
(`geom_point()`).
Code
# Fig. S1ggplot(d_rs@sam_data, aes(x = practice, y =as.numeric(Cu), fill = practice)) +geom_violin() +geom_jitter()
Warning: Removed 26 rows containing non-finite outside the scale range
(`stat_ydensity()`).
Warning: Removed 26 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning in cor.test.default(d_with_pca@sam_data$Dim.1,
d_with_pca@sam_data$nb_otu, : Impossible de calculer la p-value exacte avec des
ex-aequos
Spearman's rank correlation rho
data: d_with_pca@sam_data$Dim.1 and d_with_pca@sam_data$nb_otu
S = 20547, p-value = 0.7416
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.04831879
Warning in cor.test.default(d_with_pca@sam_data$Dim.2,
d_with_pca@sam_data$nb_otu, : Impossible de calculer la p-value exacte avec des
ex-aequos
Spearman's rank correlation rho
data: d_with_pca@sam_data$Dim.2 and d_with_pca@sam_data$nb_otu
S = 21517, p-value = 0.5037
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.09781111
Warning in cor.test.default(d_with_pca@sam_data$Dim.3,
d_with_pca@sam_data$nb_otu, : Impossible de calculer la p-value exacte avec des
ex-aequos
Spearman's rank correlation rho
data: d_with_pca@sam_data$Dim.3 and d_with_pca@sam_data$nb_otu
S = 23684, p-value = 0.1508
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.208378
Code
(ggstatsplot::ggscatterstats(psmelt_samples_pq(d_with_pca), Dim.1, Hill_0, type ="non-parametric") + ggstatsplot::ggscatterstats(psmelt_samples_pq(d_with_pca), Dim.1, Hill_1, type ="non-parametric") + ggstatsplot::ggscatterstats(psmelt_samples_pq(d_with_pca), Dim.1, Hill_2, type ="non-parametric")) / (ggstatsplot::ggscatterstats(psmelt_samples_pq(d_with_pca), Dim.2, Hill_0, type ="non-parametric") + ggstatsplot::ggscatterstats(psmelt_samples_pq(d_with_pca), Dim.2, Hill_1, type ="non-parametric") + ggstatsplot::ggscatterstats(psmelt_samples_pq(d_with_pca), Dim.2, Hill_2, type ="non-parametric"))
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Taxa are now in rows.
Joining with `by = join_by(Sample)`
Taxa are now in rows.
Joining with `by = join_by(Sample)`
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`.
Analysis of Variance Table
Response: Distances
Df Sum Sq Mean Sq F value Pr(>F)
Groups 2 0.01743 0.0087135 0.8894 0.4154
Residuals 72 0.70541 0.0097974
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).